Routine sequencing of whole genomes is not economically feasible, and as an alternative, it is often necessary to select genomic areas of interest for capture prior to sequencing. Numerous techniques have been developed for capturing target nucleic acids for subsequent detection and analysis that are compatible for use with massively parallel sequencing platforms. Such exemplary techniques include multiplex PCR capture with primer pairs and array-based or solution-based hybrid capture. Often, capture-based technologies are designed to provide a mechanism to analyze complex genomes by selecting genomic areas of interest prior to sequencing or detection. By analyzing the area of interest, the genome can be studied with significantly reduced costs and reduced time as compared with the task of sequencing large numbers of complex genomes in their entireties.
A problem with nucleic acid capture techniques is their inability to capture multiple loci with substantially uniform efficiencies. Such efficiencies define the amount of sequencing required to adequately cover the targets. Turner et al., Annu. Rev. Genomics Hum. Genet. 2009 10:263-84. Generally, the distribution of abundances of capture reaction products is rather wide, with the most and least frequent species spanning multiple orders of magnitude. Such a wide distribution in abundance means that a large number of sequencing reactions must be performed to generate an effective coverage of the target, increasing costs and time to results.